GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapF in Desulfovibrio vulgaris Miyazaki F

Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate 8499796 DvMF_0561 diaminopimelate epimerase (RefSeq)

Query= curated2:O67693
         (279 letters)



>FitnessBrowser__Miya:8499796
          Length = 282

 Score =  201 bits (512), Expect = 1e-56
 Identities = 125/279 (44%), Positives = 160/279 (57%), Gaps = 19/279 (6%)

Query: 5   KLQGSGNDFVVIDDRDEKLESFLKERGVSKEDFVRKVCAFHTGVGADGLILI-KNPDNPE 63
           KL G GNDFV ID+R   L         +  D+ R VC    GVGADGL+ + + P + E
Sbjct: 12  KLHGCGNDFVFIDNRALGLPV------AAMPDWARSVCRRAFGVGADGLVFLDETPKDRE 65

Query: 64  NDFKWEFFNSDGSVAEMCGNGSRCAVRFAYERGIVGNKVRFETLAGVIKAEVYENGRKVK 123
            D+ W F+N+DGS AEMCGN SRCA   A E G  G K  F T AG+I+AE        K
Sbjct: 66  GDYIWHFYNADGSRAEMCGNASRCAALLAVELGFAGPKHVFGTDAGLIRAEADVAAGMAK 125

Query: 124 VQLTPPSKPEEKTLTVD-----GEEVIGVFINTGVPHFVVPVEDVEKVNVIKLGRAIRFH 178
           V+LTPP    + TL ++     G +++  F+NTGVPH VV   D   V+V  LG A+R H
Sbjct: 126 VELTPP---RDLTLGIELDLGEGRDMVH-FVNTGVPHAVVFKRDASTVDVRTLGAALRRH 181

Query: 179 EEFQPKGTNVNFVQPVSEDTIKVRTYERGVESETLACGTGATACAIVSYLKGLVKKKPVN 238
             F P GTN NF Q +    I +RT+ERGVE ET ACGTGA A A +++  GL  +  VN
Sbjct: 182 AHFAPAGTNANFAQVIDRRNIHLRTFERGVEDETYACGTGAAAGAFIAHALGLA-ESTVN 240

Query: 239 VLTRSGEVLTIDFSEDLKEVFLTGSVYKVFEGRLSEEVL 277
           V +  GE+L I  S +   VFL+G   +VF G +  E L
Sbjct: 241 VRSSGGEILGI--SIEGGSVFLSGKAVRVFSGEMFLEGL 277


Lambda     K      H
   0.317    0.138    0.399 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 205
Number of extensions: 7
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 279
Length of database: 282
Length adjustment: 26
Effective length of query: 253
Effective length of database: 256
Effective search space:    64768
Effective search space used:    64768
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.7 bits)

Align candidate 8499796 DvMF_0561 (diaminopimelate epimerase (RefSeq))
to HMM TIGR00652 (dapF: diaminopimelate epimerase (EC 5.1.1.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.10049.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.10049.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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